This discussion on the fitting of Engineering into the refit hull inspired me to look at the question myself. After looking at various blueprint versions of the refit, and tracing the centerline of the struts through the centerline of the secondary hull, like this (image from memory alpha):
I have come to the conclusion that Engineering should ROUGHLY fit like so (original by Andy Probert):
This assumes two caveats:
1) That the nacelle "power conduits" run straight from the main conduit without any curves or angles through the struts to the engines.
2) That the blueprints are accurate. (FWIW, I own the TMP blueprints and Scotty's Guide and a physical check of those are consistent with what I found by examining other folks' work found online. See below.)
Anyway, I thought that this info might help with your ceiling problem...
(I looked at Shaw's Phase II stuff
, Richard Taylor's pre-greebled refit
(d/l'ed from Forgotten Trek), model photos, online blueprints like this
and printed works.)